3KWW

Crystal structure of the 'restriction triad' mutant of HLA B*3508, beta-2-microglobulin and EBV peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZHL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.62980.1M cacodlyate, 0.2M ammonium acetate, 18% PEG3350, pH 7.6, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5551.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.972α = 90
b = 81.454β = 90
c = 110.38γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2982008-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX1Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.185099.40.05716.73.32458824588
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.182.2699.93.82428

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1zhl2.1833.67245882355998999.460.1880.1860.251RANDOM17.066
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.62-0.851.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.122
r_dihedral_angle_4_deg15.875
r_dihedral_angle_3_deg13.39
r_dihedral_angle_1_deg5.563
r_scangle_it3.443
r_scbond_it2.548
r_mcangle_it1.532
r_angle_refined_deg1.04
r_mcbond_it0.954
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.122
r_dihedral_angle_4_deg15.875
r_dihedral_angle_3_deg13.39
r_dihedral_angle_1_deg5.563
r_scangle_it3.443
r_scbond_it2.548
r_mcangle_it1.532
r_angle_refined_deg1.04
r_mcbond_it0.954
r_nbtor_refined0.295
r_nbd_refined0.178
r_symmetry_vdw_refined0.153
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.114
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3177
Nucleic Acid Atoms
Solvent Atoms348
Heterogen Atoms90

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction